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Items: 1 to 50 of 186

1.

Bastion3: a two-layer ensemble predictor of type III secreted effectors.

Wang J, Li J, Yang B, Xie R, Marquez-Lago TT, Leier A, Hayashida M, Akutsu T, Zhang Y, Chou KC, Selkrig J, Zhou T, Song J, Lithgow T.

Bioinformatics. 2018 Nov 2. doi: 10.1093/bioinformatics/bty914. [Epub ahead of print]

PMID:
30388198
2.

Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods.

Li F, Wang Y, Li C, Marquez-Lago TT, Leier A, Rawlings ND, Haffari G, Revote J, Akutsu T, Chou KC, Purcell AW, Pike RN, Webb GI, Ian Smith A, Lithgow T, Daly RJ, Whisstock JC, Song J.

Brief Bioinform. 2018 Aug 29. doi: 10.1093/bib/bby077. [Epub ahead of print]

PMID:
30184176
3.

FusC, a member of the M16 protease family acquired by bacteria for iron piracy against plants.

Grinter R, Hay ID, Song J, Wang J, Teng D, Dhanesakaran V, Wilksch JJ, Davies MR, Littler D, Beckham SA, Henderson IR, Strugnell RA, Dougan G, Lithgow T.

PLoS Biol. 2018 Aug 2;16(8):e2006026. doi: 10.1371/journal.pbio.2006026. eCollection 2018 Aug.

4.

Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.

Li F, Li C, Marquez-Lago TT, Leier A, Akutsu T, Purcell AW, Smith AI, Lithgow T, Daly RJ, Song J, Chou KC.

Bioinformatics. 2018 Jun 27. doi: 10.1093/bioinformatics/bty522. [Epub ahead of print]

PMID:
29947803
5.

An investigation into the Omp85 protein BamK in hypervirulent Klebsiella pneumoniae, and its role in outer membrane biogenesis.

Vergel L Torres V, Heinz E, Stubenrauch CJ, Wilksch JJ, Cao H, Yang J, Clements A, Dunstan RA, Alcock F, Webb CT, Dougan G, Strugnell RA, Hay ID, Lithgow T.

Mol Microbiol. 2018 Sep;109(5):584-599. doi: 10.1111/mmi.13990. Epub 2018 Sep 19.

PMID:
29873128
6.

The WD40 Protein BamB Mediates Coupling of BAM Complexes into Assembly Precincts in the Bacterial Outer Membrane.

Gunasinghe SD, Shiota T, Stubenrauch CJ, Schulze KE, Webb CT, Fulcher AJ, Dunstan RA, Hay ID, Naderer T, Whelan DR, Bell TDM, Elgass KD, Strugnell RA, Lithgow T.

Cell Rep. 2018 May 29;23(9):2782-2794. doi: 10.1016/j.celrep.2018.04.093.

7.

Methionine biosynthesis and transport are functionally redundant for the growth and virulence of Salmonella Typhimurium.

Husna AU, Wang N, Cobbold SA, Newton HJ, Hocking DM, Wilksch JJ, Scott TA, Davies MR, Hinton JC, Tree JJ, Lithgow T, McConville MJ, Strugnell RA.

J Biol Chem. 2018 Jun 15;293(24):9506-9519. doi: 10.1074/jbc.RA118.002592. Epub 2018 May 2.

8.

Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa.

Zhu Y, Czauderna T, Zhao J, Klapperstueck M, Maifiah MHM, Han ML, Lu J, Sommer B, Velkov T, Lithgow T, Song J, Schreiber F, Li J.

Gigascience. 2018 Apr 1;7(4). doi: 10.1093/gigascience/giy021.

PMID:
29688451
9.

Outer membrane vesicles from Neisseria gonorrhoeae target PorB to mitochondria and induce apoptosis.

Deo P, Chow SH, Hay ID, Kleifeld O, Costin A, Elgass KD, Jiang JH, Ramm G, Gabriel K, Dougan G, Lithgow T, Heinz E, Naderer T.

PLoS Pathog. 2018 Mar 30;14(3):e1006945. doi: 10.1371/journal.ppat.1006945. eCollection 2018 Mar.

10.

Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors.

Wang J, Yang B, Leier A, Marquez-Lago TT, Hayashida M, Rocker A, Zhang Y, Akutsu T, Chou KC, Strugnell RA, Song J, Lithgow T.

Bioinformatics. 2018 Aug 1;34(15):2546-2555. doi: 10.1093/bioinformatics/bty155.

PMID:
29547915
11.

Correction for Nguyen et al., "Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers".

Nguyen S, Baker K, Padman BS, Patwa R, Dunstan RA, Weston TA, Schlosser K, Bailey B, Lithgow T, Lazarou M, Luque A, Rohwer F, Blumberg RS, Barr JJ.

MBio. 2018 Jan 2;9(1). pii: e02207-17. doi: 10.1128/mBio.02207-17. No abstract available.

12.

Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches.

Wang J, Yang B, An Y, Marquez-Lago T, Leier A, Wilksch J, Hong Q, Zhang Y, Hayashida M, Akutsu T, Webb GI, Strugnell RA, Song J, Lithgow T.

Brief Bioinform. 2017 Nov 27. doi: 10.1093/bib/bbx164. [Epub ahead of print]

PMID:
29186295
13.

Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers.

Nguyen S, Baker K, Padman BS, Patwa R, Dunstan RA, Weston TA, Schlosser K, Bailey B, Lithgow T, Lazarou M, Luque A, Rohwer F, Blumberg RS, Barr JJ.

MBio. 2017 Nov 21;8(6). pii: e01874-17. doi: 10.1128/mBio.01874-17. Erratum in: MBio. 2018 Jan 2;9(1):.

14.

Constraints on lateral gene transfer in promoting fimbrial usher protein diversity and function.

Stubenrauch CJ, Dougan G, Lithgow T, Heinz E.

Open Biol. 2017 Nov;7(11). pii: 170144. doi: 10.1098/rsob.170144.

15.

The Structure of a Conserved Domain of TamB Reveals a Hydrophobic β Taco Fold.

Josts I, Stubenrauch CJ, Vadlamani G, Mosbahi K, Walker D, Lithgow T, Grinter R.

Structure. 2017 Dec 5;25(12):1898-1906.e5. doi: 10.1016/j.str.2017.10.002. Epub 2017 Nov 9.

16.

Structure and Membrane Topography of the Vibrio-Type Secretin Complex from the Type 2 Secretion System of Enteropathogenic Escherichia coli.

Hay ID, Belousoff MJ, Dunstan RA, Bamert RS, Lithgow T.

J Bacteriol. 2018 Feb 7;200(5). pii: e00521-17. doi: 10.1128/JB.00521-17. Print 2018 Mar 1.

17.

Reductive evolution in outer membrane protein biogenesis has not compromised cell surface complexity in Helicobacter pylori.

Webb CT, Chandrapala D, Oslan SN, Bamert RS, Grinter RD, Dunstan RA, Gorrell RJ, Song J, Strugnell RA, Lithgow T, Kwok T.

Microbiologyopen. 2017 Dec;6(6). doi: 10.1002/mbo3.513. Epub 2017 Oct 21.

18.

Phylogenetic Analysis of Klebsiella pneumoniae from Hospitalized Children, Pakistan.

Ejaz H, Wang N, Wilksch JJ, Page AJ, Cao H, Gujaran S, Keane JA, Lithgow T, Ul-Haq I, Dougan G, Strugnell RA, Heinz E.

Emerg Infect Dis. 2017 Nov;23(11):1872-1875. doi: 10.3201/eid2311.170833.

19.

Structural Basis of Type 2 Secretion System Engagement between the Inner and Outer Bacterial Membranes.

Hay ID, Belousoff MJ, Lithgow T.

MBio. 2017 Oct 17;8(5). pii: e01344-17. doi: 10.1128/mBio.01344-17.

20.

The TPR domain of BepA is required for productive interaction with substrate proteins and the β-barrel assembly machinery complex.

Daimon Y, Iwama-Masui C, Tanaka Y, Shiota T, Suzuki T, Miyazaki R, Sakurada H, Lithgow T, Dohmae N, Mori H, Tsukazaki T, Narita SI, Akiyama Y.

Mol Microbiol. 2017 Dec;106(5):760-776. doi: 10.1111/mmi.13844. Epub 2017 Oct 17.

PMID:
28960545
21.

POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles.

Wang J, Yang B, Revote J, Leier A, Marquez-Lago TT, Webb G, Song J, Chou KC, Lithgow T.

Bioinformatics. 2017 Sep 1;33(17):2756-2758. doi: 10.1093/bioinformatics/btx302.

PMID:
28903538
22.

Structural basis for substrate selection by the translocation and assembly module of the β-barrel assembly machinery.

Bamert RS, Lundquist K, Hwang H, Webb CT, Shiota T, Stubenrauch CJ, Belousoff MJ, Goode RJA, Schittenhelm RB, Zimmerman R, Jung M, Gumbart JC, Lithgow T.

Mol Microbiol. 2017 Oct;106(1):142-156. doi: 10.1111/mmi.13757. Epub 2017 Aug 9.

23.

Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites.

Wang Y, Song J, Marquez-Lago TT, Leier A, Li C, Lithgow T, Webb GI, Shen HB.

Sci Rep. 2017 Jul 18;7(1):5755. doi: 10.1038/s41598-017-06219-7.

24.

Extensively Drug-Resistant Klebsiella pneumoniae Causing Nosocomial Bloodstream Infections in China: Molecular Investigation of Antibiotic Resistance Determinants, Informing Therapy, and Clinical Outcomes.

Bi W, Liu H, Dunstan RA, Li B, Torres VVL, Cao J, Chen L, Wilksch JJ, Strugnell RA, Lithgow T, Zhou T.

Front Microbiol. 2017 Jun 30;8:1230. doi: 10.3389/fmicb.2017.01230. eCollection 2017.

25.

Defining Membrane Protein Localization by Isopycnic Density Gradients.

Dunstan RA, Hay ID, Lithgow T.

Methods Mol Biol. 2017;1615:81-86. doi: 10.1007/978-1-4939-7033-9_6.

PMID:
28667604
26.

Super-Resolution Imaging of Protein Secretion Systems and the Cell Surface of Gram-Negative Bacteria.

Gunasinghe SD, Webb CT, Elgass KD, Hay ID, Lithgow T.

Front Cell Infect Microbiol. 2017 May 29;7:220. doi: 10.3389/fcimb.2017.00220. eCollection 2017. Review.

27.

Structural Basis for Linezolid Binding Site Rearrangement in the Staphylococcus aureus Ribosome.

Belousoff MJ, Eyal Z, Radjainia M, Ahmed T, Bamert RS, Matzov D, Bashan A, Zimmerman E, Mishra S, Cameron D, Elmlund H, Peleg AY, Bhushan S, Lithgow T, Yonath A.

MBio. 2017 May 9;8(3). pii: e00395-17. doi: 10.1128/mBio.00395-17.

28.

SecretEPDB: a comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems.

An Y, Wang J, Li C, Revote J, Zhang Y, Naderer T, Hayashida M, Akutsu T, Webb GI, Lithgow T, Song J.

Sci Rep. 2017 Jan 23;7:41031. doi: 10.1038/srep41031.

29.

Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI.

An Y, Wang J, Li C, Leier A, Marquez-Lago T, Wilksch J, Zhang Y, Webb GI, Song J, Lithgow T.

Brief Bioinform. 2018 Jan 1;19(1):148-161. doi: 10.1093/bib/bbw100.

PMID:
27777222
30.

GlycoMinestruct: a new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features.

Li F, Li C, Revote J, Zhang Y, Webb GI, Li J, Song J, Lithgow T.

Sci Rep. 2016 Oct 6;6:34595. doi: 10.1038/srep34595.

31.

The modular nature of the β-barrel assembly machinery, illustrated in Borrelia burgdorferi.

Stubenrauch C, Grinter R, Lithgow T.

Mol Microbiol. 2016 Dec;102(5):753-756. doi: 10.1111/mmi.13527. Epub 2016 Sep 30.

32.

Effective assembly of fimbriae in Escherichia coli depends on the translocation assembly module nanomachine.

Stubenrauch C, Belousoff MJ, Hay ID, Shen HH, Lillington J, Tuck KL, Peters KM, Phan MD, Lo AW, Schembri MA, Strugnell RA, Waksman G, Lithgow T.

Nat Microbiol. 2016 May 16;1(7):16064. doi: 10.1038/nmicrobiol.2016.64.

PMID:
27572967
33.

Eliminating Legionella by inhibiting BCL-XL to induce macrophage apoptosis.

Speir M, Lawlor KE, Glaser SP, Abraham G, Chow S, Vogrin A, Schulze KE, Schuelein R, O'Reilly LA, Mason K, Hartland EL, Lithgow T, Strasser A, Lessene G, Huang DC, Vince JE, Naderer T.

Nat Microbiol. 2016 Feb 24;1:15034. doi: 10.1038/nmicrobiol.2015.34.

PMID:
27572165
34.

Conserved Features in the Structure, Mechanism, and Biogenesis of the Inverse Autotransporter Protein Family.

Heinz E, Stubenrauch CJ, Grinter R, Croft NP, Purcell AW, Strugnell RA, Dougan G, Lithgow T.

Genome Biol Evol. 2016 Jun 13;8(6):1690-705. doi: 10.1093/gbe/evw112.

35.

Antibiotic regimen based on population analysis of residing persister cells eradicates Staphylococcus epidermidis biofilms.

Yang S, Hay ID, Cameron DR, Speir M, Cui B, Su F, Peleg AY, Lithgow T, Deighton MA, Qu Y.

Sci Rep. 2015 Dec 21;5:18578. doi: 10.1038/srep18578.

36.

Identification of BamC on the Surface of E. coli.

Webb CT, Lithgow T.

Methods Mol Biol. 2015;1329:215-25. doi: 10.1007/978-1-4939-2871-2_17.

PMID:
26427688
37.

The β-Barrel Assembly Machinery Complex.

Leyton DL, Belousoff MJ, Lithgow T.

Methods Mol Biol. 2015;1329:1-16. doi: 10.1007/978-1-4939-2871-2_1. Review.

PMID:
26427672
38.

Molecular architecture of the active mitochondrial protein gate.

Shiota T, Imai K, Qiu J, Hewitt VL, Tan K, Shen HH, Sakiyama N, Fukasawa Y, Hayat S, Kamiya M, Elofsson A, Tomii K, Horton P, Wiedemann N, Pfanner N, Lithgow T, Endo T.

Science. 2015 Sep 25;349(6255):1544-8. doi: 10.1126/science.aac6428.

PMID:
26404837
39.

Evidence of Distinct Channel Conformations and Substrate Binding Affinities for the Mitochondrial Outer Membrane Protein Translocase Pore Tom40.

Kuszak AJ, Jacobs D, Gurnev PA, Shiota T, Louis JM, Lithgow T, Bezrukov SM, Rostovtseva TK, Buchanan SK.

J Biol Chem. 2015 Oct 23;290(43):26204-17. doi: 10.1074/jbc.M115.642173. Epub 2015 Sep 2.

40.

Conserved features in TamA enable interaction with TamB to drive the activity of the translocation and assembly module.

Selkrig J, Belousoff MJ, Headey SJ, Heinz E, Shiota T, Shen HH, Beckham SA, Bamert RS, Phan MD, Schembri MA, Wilce MC, Scanlon MJ, Strugnell RA, Lithgow T.

Sci Rep. 2015 Aug 5;5:12905. doi: 10.1038/srep12905.

41.

Evolution of the Translocation and Assembly Module (TAM).

Heinz E, Selkrig J, Belousoff MJ, Lithgow T.

Genome Biol Evol. 2015 May 20;7(6):1628-43. doi: 10.1093/gbe/evv097.

42.

Assembly of the secretion pores GspD, Wza and CsgG into bacterial outer membranes does not require the Omp85 proteins BamA or TamA.

Dunstan RA, Hay ID, Wilksch JJ, Schittenhelm RB, Purcell AW, Clark J, Costin A, Ramm G, Strugnell RA, Lithgow T.

Mol Microbiol. 2015 Aug;97(4):616-29. doi: 10.1111/mmi.13055. Epub 2015 Jun 6.

43.

Positive autoregulation of mrkHI by the cyclic di-GMP-dependent MrkH protein in the biofilm regulatory circuit of Klebsiella pneumoniae.

Tan JW, Wilksch JJ, Hocking DM, Wang N, Srikhanta YN, Tauschek M, Lithgow T, Robins-Browne RM, Yang J, Strugnell RA.

J Bacteriol. 2015 May;197(9):1659-67. doi: 10.1128/JB.02615-14. Epub 2015 Mar 2.

44.

Mitochondrial biogenesis: cell-cycle-dependent investment in making mitochondria.

Shiota T, Traven A, Lithgow T.

Curr Biol. 2015 Jan 19;25(2):R78-R80. doi: 10.1016/j.cub.2014.12.006.

45.

Of linkers and autochaperones: an unambiguous nomenclature to identify common and uncommon themes for autotransporter secretion.

Drobnak I, Braselmann E, Chaney JL, Leyton DL, Bernstein HD, Lithgow T, Luirink J, Nataro JP, Clark PL.

Mol Microbiol. 2015 Jan;95(1):1-16. doi: 10.1111/mmi.12838. Epub 2014 Nov 24. Review.

46.

Reconstitution of a nanomachine driving the assembly of proteins into bacterial outer membranes.

Shen HH, Leyton DL, Shiota T, Belousoff MJ, Noinaj N, Lu J, Holt SA, Tan K, Selkrig J, Webb CT, Buchanan SK, Martin LL, Lithgow T.

Nat Commun. 2014 Oct 24;5:5078. doi: 10.1038/ncomms6078.

47.

A comprehensive analysis of the Omp85/TpsB protein superfamily structural diversity, taxonomic occurrence, and evolution.

Heinz E, Lithgow T.

Front Microbiol. 2014 Jul 21;5:370. doi: 10.3389/fmicb.2014.00370. eCollection 2014.

48.

A mortise-tenon joint in the transmembrane domain modulates autotransporter assembly into bacterial outer membranes.

Leyton DL, Johnson MD, Thapa R, Huysmans GH, Dunstan RA, Celik N, Shen HH, Loo D, Belousoff MJ, Purcell AW, Henderson IR, Beddoe T, Rossjohn J, Martin LL, Strugnell RA, Lithgow T.

Nat Commun. 2014 Jun 26;5:4239. doi: 10.1038/ncomms5239.

PMID:
24967730
49.

Efficient construction of unmarked recombinant mycobacteria using an improved system.

Yang F, Tan Y, Liu J, Liu T, Wang B, Cao Y, Qu Y, Lithgow T, Tan S, Zhang T.

J Microbiol Methods. 2014 Aug;103:29-36. doi: 10.1016/j.mimet.2014.05.007. Epub 2014 May 27.

PMID:
24873745
50.

Transcriptional activation of the mrkA promoter of the Klebsiella pneumoniae type 3 fimbrial operon by the c-di-GMP-dependent MrkH protein.

Yang J, Wilksch JJ, Tan JW, Hocking DM, Webb CT, Lithgow T, Robins-Browne RM, Strugnell RA.

PLoS One. 2013 Nov 14;8(11):e79038. doi: 10.1371/journal.pone.0079038. eCollection 2013.

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